[2023-06-30 10:57:31,544] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:57:31,547] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:57:31,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg05761cbc-7ef8-452c-91df-5e53ddf26d93/dqc_reference
[2023-06-30 10:57:33,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:57:33,380] [INFO] Task started: Prodigal
[2023-06-30 10:57:33,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg50aee922-4297-493e-a573-e196c772b72b/GCA_024693545.1_ASM2469354v1_genomic.fna.gz | prodigal -d GCA_024693545.1_ASM2469354v1_genomic.fna/cds.fna -a GCA_024693545.1_ASM2469354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:57:37,817] [INFO] Task succeeded: Prodigal
[2023-06-30 10:57:37,818] [INFO] Task started: HMMsearch
[2023-06-30 10:57:37,818] [INFO] Running command: hmmsearch --tblout GCA_024693545.1_ASM2469354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05761cbc-7ef8-452c-91df-5e53ddf26d93/dqc_reference/reference_markers.hmm GCA_024693545.1_ASM2469354v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:57:37,988] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:57:37,989] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg50aee922-4297-493e-a573-e196c772b72b/GCA_024693545.1_ASM2469354v1_genomic.fna.gz]
[2023-06-30 10:57:38,009] [INFO] Query marker FASTA was written to GCA_024693545.1_ASM2469354v1_genomic.fna/markers.fasta
[2023-06-30 10:57:38,010] [INFO] Task started: Blastn
[2023-06-30 10:57:38,010] [INFO] Running command: blastn -query GCA_024693545.1_ASM2469354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05761cbc-7ef8-452c-91df-5e53ddf26d93/dqc_reference/reference_markers.fasta -out GCA_024693545.1_ASM2469354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:57:38,544] [INFO] Task succeeded: Blastn
[2023-06-30 10:57:38,548] [INFO] Selected 18 target genomes.
[2023-06-30 10:57:38,549] [INFO] Target genome list was writen to GCA_024693545.1_ASM2469354v1_genomic.fna/target_genomes.txt
[2023-06-30 10:57:38,571] [INFO] Task started: fastANI
[2023-06-30 10:57:38,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg50aee922-4297-493e-a573-e196c772b72b/GCA_024693545.1_ASM2469354v1_genomic.fna.gz --refList GCA_024693545.1_ASM2469354v1_genomic.fna/target_genomes.txt --output GCA_024693545.1_ASM2469354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:57:48,691] [INFO] Task succeeded: fastANI
[2023-06-30 10:57:48,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05761cbc-7ef8-452c-91df-5e53ddf26d93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:57:48,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05761cbc-7ef8-452c-91df-5e53ddf26d93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:57:48,693] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:57:48,693] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:57:48,693] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-30 10:57:48,695] [INFO] DFAST Taxonomy check result was written to GCA_024693545.1_ASM2469354v1_genomic.fna/tc_result.tsv
[2023-06-30 10:57:48,696] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:57:48,696] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:57:48,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05761cbc-7ef8-452c-91df-5e53ddf26d93/dqc_reference/checkm_data
[2023-06-30 10:57:48,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:57:48,724] [INFO] Task started: CheckM
[2023-06-30 10:57:48,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024693545.1_ASM2469354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024693545.1_ASM2469354v1_genomic.fna/checkm_input GCA_024693545.1_ASM2469354v1_genomic.fna/checkm_result
[2023-06-30 10:58:08,707] [INFO] Task succeeded: CheckM
[2023-06-30 10:58:08,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.28%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 10:58:08,739] [INFO] ===== Completeness check finished =====
[2023-06-30 10:58:08,739] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:58:08,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024693545.1_ASM2469354v1_genomic.fna/markers.fasta)
[2023-06-30 10:58:08,740] [INFO] Task started: Blastn
[2023-06-30 10:58:08,740] [INFO] Running command: blastn -query GCA_024693545.1_ASM2469354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05761cbc-7ef8-452c-91df-5e53ddf26d93/dqc_reference/reference_markers_gtdb.fasta -out GCA_024693545.1_ASM2469354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:58:09,483] [INFO] Task succeeded: Blastn
[2023-06-30 10:58:09,489] [INFO] Selected 19 target genomes.
[2023-06-30 10:58:09,490] [INFO] Target genome list was writen to GCA_024693545.1_ASM2469354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:58:09,500] [INFO] Task started: fastANI
[2023-06-30 10:58:09,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg50aee922-4297-493e-a573-e196c772b72b/GCA_024693545.1_ASM2469354v1_genomic.fna.gz --refList GCA_024693545.1_ASM2469354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024693545.1_ASM2469354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:58:17,787] [INFO] Task succeeded: fastANI
[2023-06-30 10:58:17,792] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 10:58:17,793] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_016285135.1	s__RUG11977 sp016285135	79.85	270	625	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	98.61	98.52	0.82	0.80	3	-
GCA_017427685.1	s__RUG11977 sp017427685	79.6249	301	625	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	96.94	96.87	0.89	0.88	3	-
GCA_016281275.1	s__RUG11977 sp016281275	79.5847	256	625	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288005.1	s__RUG11977 sp016288005	77.0534	55	625	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	96.56	96.56	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-30 10:58:17,797] [INFO] GTDB search result was written to GCA_024693545.1_ASM2469354v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:58:17,799] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:58:17,801] [INFO] DFAST_QC result json was written to GCA_024693545.1_ASM2469354v1_genomic.fna/dqc_result.json
[2023-06-30 10:58:17,802] [INFO] DFAST_QC completed!
[2023-06-30 10:58:17,802] [INFO] Total running time: 0h0m46s